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a strategic consultant in mobile health. He was searching for technologies that could help remote clinics diagnose tuberculosis. In assessing the feasibility of gene sequencing, he realized there was a bottleneck in processing the genomic data.

“The idea was to build a processor that could replace all the servers,” van Rooyen said.

He returned to San Diego to start Edico Genome in early 2013 with co-founders Robert McMillen and Michael Ruehle, who are both systems architects with many patents in a variety of computer-related technologies.

Van Rooyen, who is named on more than 110 patent filings, has lived and worked in San Diego for over a decade. He was previously a co-founder of San Diego-based ecoATM, the mobile device recycling startup acquired for $350 million in 2013 by Outerwall (NASDAQ: OUTR), and San Diego’s Zyray Wireless, a fabless provider of wireless processors that was acquired by Broadcom (NASDAQ: BRCM) for $100 million in 2004.

The co-founders provided Edico’s initial funding, and later raised some additional funding from friends and family and Qualcomm Labs. The company has adopted a lean business model, and has shaved some operating costs after it was admitted to EvoNexus, the free incubator operated by San Diego’s CommNexus industry group.

Still, FPGA processors can be relatively expensive, and one expert has questioned whether Edico’s technology can be commercialized at an affordable price. But Hunkapiller said cost is unlikely to be much of a factor for Edico, in part because the company already is moving its design to a standard ASIC (Application Specific Integrated Circuit) processor, which typically can be mass-produced at low cost.

“There are other appliances out there [to accelerate genomic data processing] Hunkapiller said. “But nobody has been able to get significant market share. They add speed, but they do not address the cost issue.”

Van Rooyen’s commercialization plan calls for mounting the Dragen processor on cards that have been customized to work with specific genome sequencing machines, such as Illumina’s HiSeq X Ten. The company has working prototypes, and van Rooyen says, “We already have alpha customers signed up.”

By using Edico’s technology, van Rooyen says a facility using Illumina’s HiSeq X Ten machines to sequence 150 human genomes every three days would be able to save $6 million over a four-year period.

That would make it easier for hospitals and other healthcare providers to use genome sequencing to better diagnose heart disease, inflammatory disease, prenatal disease, and other conditions, van Rooyen said. “What we enable are the resources for clinical genomics,” he said. “It’s a lot easier for companies to test for all these things, because it would be a lot cheaper.”